Introduction

NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. This document describes how to use NAMD, its features, and the platforms on which it runs. The document is divided into several sections:

Section 1

gives an overview of NAMD.

Section 2

lists the basics for getting started.

Section 3

describes NAMD file formats.

Section 4

explains PSF file generation with psfgen.

Section 5

presents the potential functions, non-bonded interactions, and full electrostatics.

Section 6

explains Generalized Born implicit solvent simulations.

Section 7

lists standard minimization and dynamics parameters.

Section 8

lists performance tuning parameters.

Section 9

explains user defined forces. conformation change calculations.

Section 10

describes collective variable-based calculations.

Section 11

explains alchemical free energy calculations.

Section 12

presents accelerated sampling methods.

Section 15

lists runtime analysis options.

Section 16

provides hints for X-PLOR users.

Section 17

provides sample configuration files.

Section 18

gives details on running NAMD.

Section 19

gives details on installing NAMD.